Contacts of the helix formed by residues 55 - 67 (chain V) in PDB entry 4GGF
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 55 (chain V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97T GLY 5.3 0.2 + - - -
99T GLU* 2.8 26.8 + - - +
51V LYS 5.0 2.2 - - - +
52V GLU 3.0 12.5 + - - +
53V ASN 3.1 2.0 - - - -
54V LYS* 1.3 80.8 - - + +
56V GLU* 1.3 64.9 + - - +
57V LYS* 3.1 24.1 + - - +
58V VAL* 3.0 36.4 + - + +
59V ILE* 3.1 11.0 + - - +
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Residues in contact with GLU 56 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38V LYS* 2.8 42.0 + - + +
53V ASN 4.9 1.9 + - - -
54V LYS 4.0 2.2 + - - -
55V ASN* 1.3 73.2 + - - +
57V LYS* 1.3 75.4 + - + +
59V ILE* 3.3 6.8 + - + +
60V GLU* 2.9 37.1 + - - +
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Residues in contact with LYS 57 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99T GLU* 3.7 36.7 - - + +
55V ASN* 3.1 12.5 + - - +
56V GLU* 1.3 92.7 + - + +
58V VAL* 1.3 61.8 + - - +
60V GLU* 3.1 39.5 + - - +
61V HIS* 3.0 26.9 + - - +
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Residues in contact with VAL 58 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97T GLY* 3.9 31.0 - - - +
98T ASP 3.7 12.7 - - - +
99T GLU* 4.2 2.2 - - + -
52V GLU* 3.9 35.7 - - + -
55V ASN* 3.0 39.7 + - + +
57V LYS* 1.3 77.8 - - - +
59V ILE* 1.3 63.8 + - - +
61V HIS* 3.2 5.0 + - - +
62V ILE* 3.1 26.9 + - + +
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Residues in contact with ILE 59 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37V PHE* 3.9 17.3 - - + -
38V LYS* 3.9 31.4 - - + -
41V VAL* 3.7 25.1 - - + -
49V LEU* 5.1 0.9 - - + -
52V GLU* 3.6 35.7 - - + +
53V ASN* 3.8 13.9 - - - +
55V ASN 3.1 14.1 + - - +
56V GLU* 3.7 9.6 - - + +
57V LYS 3.3 0.2 - - - -
58V VAL* 1.3 75.8 - - - +
60V GLU* 1.3 64.0 + - - +
62V ILE* 3.2 13.3 + - + +
63V MET* 3.0 21.7 + - - +
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Residues in contact with GLU 60 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34V GLN* 3.5 28.0 + - - +
38V LYS* 2.7 32.3 + - - +
56V GLU* 2.9 16.1 + - - +
57V LYS* 3.1 42.0 + - - +
59V ILE* 1.3 77.8 - - - +
61V HIS* 1.3 61.0 + - - +
63V MET* 3.3 5.3 + - - +
64V GLU* 3.0 35.2 + - - +
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Residues in contact with HIS 61 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26S PHE* 5.7 6.5 - + - -
27S HIS* 5.3 3.1 - + - -
95T HIS* 4.0 20.2 + + - +
98T ASP* 3.0 60.1 + - + +
99T GLU 4.4 5.2 - - - -
100T GLY* 4.5 4.6 + - - -
102T GLY 4.6 12.7 + - - -
103T HIS* 6.0 0.7 - + - -
205T GOL 5.2 4.4 + - - -
57V LYS 3.0 12.3 + - - +
58V VAL* 3.2 4.9 + - + +
60V GLU* 1.3 73.1 - - - +
62V ILE* 1.3 66.6 + - + +
64V GLU* 3.2 18.1 + - - +
65V ASP* 2.8 42.2 + - + +
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Residues in contact with ILE 62 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37V PHE* 3.9 12.6 - - + -
49V LEU* 4.8 11.9 - - + -
52V GLU* 4.2 27.8 - - + -
58V VAL* 3.1 21.1 + - + +
59V ILE* 3.2 17.0 + - + +
61V HIS* 1.3 79.8 - - + +
63V MET* 1.3 65.4 + - - +
65V ASP* 3.2 7.6 + - + +
66V LEU* 3.0 42.1 + - + +
82V LEU* 4.3 15.7 - - + -
85V ARG* 6.0 1.6 - - - +
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Residues in contact with MET 63 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32V LEU 3.6 18.6 - - - +
34V GLN* 3.7 35.9 - - + +
37V PHE* 3.8 36.5 - - + -
59V ILE 3.0 12.1 + - - +
60V GLU* 3.4 9.6 - - - +
62V ILE* 1.3 76.9 - - - +
64V GLU* 1.3 65.2 + - + +
66V LEU* 3.2 7.5 + - - +
67V ASP* 3.1 24.5 + - + +
72V LYS* 3.6 32.3 - - - +
73V GLN* 4.0 1.3 - - - +
74V LEU* 3.6 23.0 - - + +
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Residues in contact with GLU 64 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25S ASN* 3.0 16.5 + - - -
26S PHE* 4.7 17.2 - - + -
101T PRO* 5.9 3.2 - - - +
102T GLY 5.1 6.6 + - - +
34V GLN* 5.6 2.7 - - - +
60V GLU* 3.0 27.7 + - + +
61V HIS* 3.5 18.3 + - - +
63V MET* 1.3 79.3 - - + +
65V ASP* 1.3 62.7 + - - +
67V ASP* 3.4 12.2 + - - +
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Residues in contact with ASP 65 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25S ASN* 2.9 21.8 + - - +
27S HIS* 2.8 37.5 + - - +
205T GOL 3.0 15.9 + - - -
61V HIS* 2.8 32.7 + - + +
62V ILE* 3.2 9.8 + - - +
64V GLU* 1.3 73.4 - - - +
66V LEU* 1.3 57.4 + - - +
68V THR* 4.3 5.4 - - - +
85V ARG* 2.9 33.6 + - - -
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Residues in contact with LEU 66 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37V PHE* 4.0 15.5 - - + -
62V ILE* 3.0 36.0 + - + +
63V MET 3.2 4.5 + - - +
65V ASP* 1.3 76.1 - - - +
67V ASP* 1.3 58.1 + - - +
68V THR* 3.0 14.3 + - - +
74V LEU* 3.7 20.2 - - + -
78V GLU* 3.2 41.1 - - - +
79V PHE* 5.2 1.3 - - - -
81V MET* 4.3 2.7 - - + -
82V LEU* 3.8 35.2 - - + +
85V ARG* 3.7 31.4 - - - +
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Residues in contact with ASP 67 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25S ASN* 3.1 13.3 + - - +
63V MET* 3.1 17.7 + - + +
64V GLU* 3.8 9.4 - - - +
65V ASP 3.3 1.8 - - - -
66V LEU* 1.3 73.4 - - - +
68V THR* 1.3 60.9 + - - +
69V ASN* 3.2 6.9 - - - +
70V ALA* 3.2 15.6 + - - -
71V ASP* 3.3 4.2 + - - +
72V LYS* 2.8 30.5 + - - +
73V GLN 3.6 7.6 - - - -
74V LEU* 3.7 11.4 - - + -
78V GLU* 3.9 1.6 - - - -
203V CA 2.3 30.6 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il